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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $species_info = array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ) $local_species = 'ugi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $species_info = array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ) $local_species = 'ugi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ), 'gf_id' => 'HOM05D001195', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001195' ), 'data_identifier' => 'HOM05D001195', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001195', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p10490' => 'bna', 'A01p10850' => 'bna', 'A01p16100' => 'bna', 'A02p32900' => 'bna', 'A02p32910' => 'bna', 'A03p55540' => 'bna', 'A06p10490' => 'bna', 'A06p43600' => 'bna', 'A06p46420' => 'bna', 'A09p21890' => 'bna', 'Aa31LG1G590' => 'aar', 'Aa31LG2G7640' => 'aar', 'Aa31LG6G1530' => 'aar', 'Aa31LG7G11050' => 'aar', 'Aa31LG9G7340' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1849' => 'aag', 'Actinidia00140' => 'ach', 'Actinidia00141' => 'ach', 'Actinidia07652' => 'ach', 'Actinidia07653' => 'ach', 'Actinidia08848' => 'ach', 'Actinidia11728' => 'ach', 'Actinidia15533' => 'ach', 'Actinidia17101' => 'ach', 'Actinidia35607' => 'ach', 'Actinidia36772' => 'ach', 'Actinidia39523' => 'ach', 'Actinidia39524' => 'ach', 'Ah.08g218340' => 'amhyb', 'AL1G26360' => 'aly', 'AL5G11750' => 'aly', 'AL7G28400' => 'aly', 'AL7G35420' => 'aly', 'AL8G12920' => 'aly', 'Aqoxy4G00234' => 'aox', 'Aqoxy5G00904' => 'aox', 'Aqoxy5G03623' => 'aox', 'Aqoxy6G00016' => 'aox', 'arahy.Tifrunner.gnm1.ann1.62B5VH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GAN3W4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GTV6YM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJZ3ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IYN8K7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRCY3Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PIT7JA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY7Z8Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4R6KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8EK17' => 'arhy', 'AT1G14460' => 'ath', 'AT2G02480' => 'ath', 'AT4G18820' => 'ath', 'AT4G24790' => 'ath', 'AT5G45720' => 'ath', 'ATR0012G006' => 'atr', 'ATR0602G253' => 'atr', 'ATR0605G234' => 'atr', 'ATR0824G094' => 'atr', 'ATR1089G146' => 'atr', 'Atru.chr10.1552' => 'acertr', 'Atru.chr13.4' => 'acertr', 'Atru.chr6.140' => 'acertr', 'Atru.chr6.141' => 'acertr', 'Atru.chr9.984' => 'acertr', 'AUR62001256' => 'cqu', 'AUR62018260' => 'cqu', 'AUR62025752' => 'cqu', 'AUR62032487' => 'cqu', 'AUR62039487' => 'cqu', 'AUR62041813' => 'cqu', 'AUR62042245' => 'cqu', 'BcaB02g06496' => 'bca', 'BcaB07g30871' => 'bca', 'BcaC03g17144' => 'bca', 'BcaC04g21747' => 'bca', 'BcaC05g25350' => 'bca', 'BcaC06g31229' => 'bca', 'BcaC06g31230' => 'bca', 'BcaC06g31521' => 'bca', 'BcaC06g32858' => 'bca', 'BcaC06g34050' => 'bca', 'BcaC06g34409' => 'bca', 'BcaC09g50829' => 'bca', 'BcaC09g51447' => 'bca', 'BcaNung04862' => 'bca', 'BcaNung05732' => 'bca', 'BolC1t01262H' => 'bol', 'BolC1t01938H' => 'bol', 'BolC2t11147H' => 'bol', 'BolC5t29981H' => 'bol', 'BolC7t43439H' => 'bol', 'BolC7t43837H' => 'bol', 'BolC7t45869H' => 'bol', 'BolC9t55673H' => 'bol', 'BraA01t00995Z' => 'bra', 'BraA01t01032Z' => 'bra', 'BraA01t01545Z' => 'bra', 'BraA01t01546Z' => 'bra', 'BraA02t08311Z' => 'bra', 'BraA03t14624Z' => 'bra', 'BraA06t24229Z' => 'bra', 'BraA06t27243Z' => 'bra', 'BraA06t27506Z' => 'bra', 'BraA09t37792Z' => 'bra', 'C01p12860' => 'bna', 'C01p20090' => 'bna', 'C02p50640' => 'bna', 'C05p12290' => 'bna', 'C07p29000' => 'bna', 'C07p33260' => 'bna', 'C07p53790' => 'bna', 'C09p28060' => 'bna', 'CAN.G1379.9' => 'can', 'CAN.G411.42' => 'can', 'CAN.G472.52' => 'can', 'CANSAT01G3051' => 'cansat', 'CANSAT35G1100' => 'cansat', 'CANSAT80G2654' => 'cansat', 'CARHR014920' => 'chi', 'CARHR145020' => 'chi', 'CARHR145040' => 'chi', 'CARHR176250' => 'chi', 'CARHR225680' => 'chi', 'CARHR232170' => 'chi', 'Carub.0001s1418' => 'cru', 'Carub.0005s0149' => 'cru', 'Carub.0007s1627' => 'cru', 'Carub.0007s2241' => 'cru', 'Carub.0008s0227' => 'cru', 'Ca_00474_v3' => 'car', 'Ca_13522_v3' => 'car', 'Ca_16103_v3' => 'car', 'Ca_26534_v3' => 'car', 'Ca_30079_v3' => 'car', 'CBR_g48156' => 'cbr', 'CBR_g8413' => 'cbr', 'Cc02_g15690' => 'ccan', 'Cc02_g15700' => 'ccan', 'Cc02_g23760' => 'ccan', 'Cc04_g10730' => 'ccan', 'CDE02G2242' => 'cde', 'CDE02G2658' => 'cde', 'CDE02G3728' => 'cde', 'CDE04G0834' => 'cde', 'CDE04G1754' => 'cde', 'CDE04G2297' => 'cde', 'CDE04G2419' => 'cde', 'CDE06G0606' => 'cde', 'CDE07G0735' => 'cde', 'Cfa001104' => 'cfa', 'Cfa004422' => 'cfa', 'Cfa018909' => 'cfa', 'Ciclev10000047m.g' => 'ccl', 'Ciclev10014075m.g' => 'ccl', 'Ciclev10018826m.g' => 'ccl', 'CiPaw.06G176900' => 'cil', 'CiPaw.09G136800' => 'cil', 'CiPaw.10G103700' => 'cil', 'CiPaw.10G103800' => 'cil', 'CiPaw.12G034000' => 'cil', 'CiPaw.12G034100' => 'cil', 'ClCG01G023950' => 'cla', 'ClCG10G007550' => 'cla', 'COL.COLO4_31209' => 'col', 'COL.COLO4_31221' => 'col', 'Cpa.g.c44482' => 'cpa', 'Cpa.g.sc173.1' => 'cpa', 'Cpa.g.sc4.39' => 'cpa', 'Cpa.g.sc7.115' => 'cpa', 'CsaV3_3G006750' => 'csa', 'CsaV3_6G051090' => 'csa', 'CSS0006950' => 'camsi', 'CSS0008302' => 'camsi', 'CSS0009860' => 'camsi', 'CSS0017629' => 'camsi', 'CSS0020747' => 'camsi', 'CSS0023410' => 'camsi', 'CSS0029612' => 'camsi', 'DCAR_001734' => 'dca', 'DCAR_003272' => 'dca', 'DCAR_005162' => 'dca', 'DCAR_007464' => 'dca', 'DCAR_027972' => 'dca', 'DCAR_032000' => 'dca', 'Dinv05526' => 'din', 'Dinv11121' => 'din', 'Dinv12743' => 'din', 'Dinv29569' => 'din', 'Dinv29651' => 'din', 'Dinv32331' => 'din', 'Dinv32332' => 'din', 'Dinv38444' => 'din', 'Dinv38491' => 'din', 'Duzib068G1230' => 'dzi', 'Duzib160G0423' => 'dzi', 'Duzib160G0611' => 'dzi', 'Duzib192G0212' => 'dzi', 'Duzib192G1074' => 'dzi', 'Duzib205G1555' => 'dzi', 'Duzib235G0195' => 'dzi', 'ECA232G2468' => 'eca', 'ECA234G3008' => 'eca', 'ECA236G0676' => 'eca', 'EL10Ac6g13960' => 'bvu', 'EL10Ac7g18047' => 'bvu', 'EL10Ac8g19988' => 'bvu', 'Eucgr.D00435' => 'egr', 'Eucgr.I02805' => 'egr', 'Eucgr.K02767' => 'egr', 'FAN04G1500' => 'fan', 'FAN04G3020' => 'fan', 'FAN08G1115' => 'fan', 'FAN08G1514' => 'fan', 'FAN08G2082' => 'fan', 'FAN08G2189' => 'fan', 'FAN11G0143' => 'fan', 'FAN13G0562' => 'fan', 'FAN13G1627' => 'fan', 'FAN13G2666' => 'fan', 'FAN16G0685' => 'fan', 'FAN18G2554' => 'fan', 'FAN18G2953' => 'fan', 'FAN18G4100' => 'fan', 'FAN21G1686' => 'fan', 'FAN25G2492' => 'fan', 'FvH4_3g07230' => 'fve', 'FvH4_5g06830' => 'fve', 'FvH4_5g06841' => 'fve', 'FvH4_5g27010' => 'fve', 'FvH4_5g27450' => 'fve', 'Glyma.04G191200' => 'gma', 'Glyma.05G044100' => 'gma', 'Glyma.06G174600' => 'gma', 'Glyma.07G271700' => 'gma', 'Glyma.13G226500' => 'gma', 'Glyma.15G085900' => 'gma', 'Glyma.17G002500' => 'gma', 'Glyma.17G126600' => 'gma', 'Gohir.A06G199200' => 'ghi', 'Gohir.A07G054400' => 'ghi', 'Gohir.A09G074900' => 'ghi', 'Gohir.A10G034100' => 'ghi', 'Gohir.A10G157700' => 'ghi', 'Gohir.D06G206500' => 'ghi', 'Gohir.D07G058700' => 'ghi', 'Gohir.D09G074700' => 'ghi', 'Gohir.D10G034800' => 'ghi', 'Gohir.D10G083300' => 'ghi', 'Gorai.001G062200' => 'gra', 'Gorai.006G089800' => 'gra', 'Gorai.010G240900' => 'gra', 'Gorai.011G036600' => 'gra', 'Gorai.011G090600' => 'gra', 'GSVIVG01007580001' => 'vvi', 'GSVIVG01021264001' => 'vvi', 'GSVIVG01023130001' => 'vvi', 'HanXRQChr09g0272761' => 'han', 'HanXRQChr13g0392341' => 'han', 'HanXRQChr14g0427521' => 'han', 'HanXRQChr15g0469651' => 'han', 'HanXRQChr17g0556931' => 'han', 'Haze_05390' => 'cav', 'Haze_07293' => 'cav', 'Haze_09962' => 'cav', 'Hma1.2p1_0157F.1_g069180' => 'hma', 'Hma1.2p1_0508F.1_g168710' => 'hma', 'Hma1.2p1_0914F.1_g236250' => 'hma', 'HPP92_013450' => 'vpl', 'HPP92_013455' => 'vpl', 'HPP92_021436' => 'vpl', 'HPP92_022985' => 'vpl', 'HPP92_023735' => 'vpl', 'HPP92_023738' => 'vpl', 'HPP92_023739' => 'vpl', 'HPP92_023740' => 'vpl', 'HPP92_027097' => 'vpl', 'Hund05619' => 'sun', 'Hund15285' => 'sun', 'Hund21450' => 'sun', 'Lalb_Chr07g0176841' => 'lal', 'Lalb_Chr07g0183201' => 'lal', 'Lalb_Chr13g0304431' => 'lal', 'Lalb_Chr15g0086351' => 'lal', 'Lalb_Chr18g0054791' => 'lal', 'Lalb_Chr21g0313571' => 'lal', 'Lalb_Chr21g0313581' => 'lal', 'Lj1A1176T61' => 'lonja', 'Lj1g0009618' => 'lja', 'Lj2A317G40' => 'lonja', 'Lj4A619T11' => 'lonja', 'Lj4g0024332' => 'lja', 'Lj4g0027334' => 'lja', 'Lj4P619T10' => 'lonja', 'Lj6g0025795' => 'lja', 'Lj9A228G12' => 'lonja', 'Lj9A253G54' => 'lonja', 'Lj9C253G11' => 'lonja', 'Lj9C473T2' => 'lonja', 'Lsat_1_v5_gn_1_122401' => 'lsa', 'Lsat_1_v5_gn_2_2301' => 'lsa', 'Lsat_1_v5_gn_3_104720' => 'lsa', 'Lsat_1_v5_gn_3_131641' => 'lsa', 'Lsat_1_v5_gn_3_38961' => 'lsa', 'Lsat_1_v5_gn_3_59501' => 'lsa', 'Lsat_1_v5_gn_3_67820' => 'lsa', 'Lsat_1_v5_gn_4_137040' => 'lsa', 'Lsat_1_v5_gn_4_48381' => 'lsa', 'Lsat_1_v5_gn_4_78221' => 'lsa', 'Lsat_1_v5_gn_6_3941' => 'lsa', 'Lsat_1_v5_gn_9_83160' => 'lsa', 'Manes.06G013800' => 'mes', 'Manes.06G113300' => 'mes', 'Manes.08G042333' => 'mes', 'Manes.14G146300' => 'mes', 'Manes.16G042500' => 'mes', 'Manes.17G059900' => 'mes', 'Manes.18G000102' => 'mes', 'Manes.18G000152' => 'mes', 'Mapoly0019s0074' => 'mpo', 'MBI01_g32835_MAGBIO' => 'mbi', 'MBI06_g12149_MAGBIO' => 'mbi', 'MBI06_g16702_MAGBIO' => 'mbi', 'MBI06_g17066_MAGBIO' => 'mbi', 'MBI06_g18695_MAGBIO' => 'mbi', 'MBI07_g00451_MAGBIO' => 'mbi', 'MD00G1008200' => 'mdo', 'MD06G1160000' => 'mdo', 'MD08G1249500' => 'mdo', 'MD10G1274700' => 'mdo', 'MD14G1166000' => 'mdo', 'Medtr2g017980' => 'mtr', 'Medtr3g075260' => 'mtr', 'Medtr4g104350' => 'mtr', 'Medtr4g134530' => 'mtr', 'MELO3C007194.2' => 'cme', 'MELO3C016434.2' => 'cme', 'Migut.H01406' => 'egut', 'Migut.N00869' => 'egut', 'Migut.O00222' => 'egut', 'Migut.O00805' => 'egut', 'MSTRG.13236' => 'ama', 'MSTRG.20342' => 'ama', 'MSTRG.23187' => 'ama', 'MSTRG.27887' => 'ama', 'MSTRG.5186' => 'ama', 'MSTRG.9701' => 'ama', 'Nitab4.5_0000437g0030' => 'nta', 'Nitab4.5_0001085g0120' => 'nta', 'Nitab4.5_0001360g0180' => 'nta', 'Nitab4.5_0006070g0030' => 'nta', 'Nitab4.5_0006159g0040' => 'nta', 'Nitab4.5_0006717g0010' => 'nta', 'Nn3g16618' => 'nnu', 'Nn3g21089' => 'nnu', 'Nn4g22512' => 'nnu', 'Nn5g27132' => 'nnu', 'Nn6g34481' => 'nnu', 'Oeu010606.1' => 'oeu', 'Oeu016649.1' => 'oeu', 'Oeu039873.1' => 'oeu', 'Oeu040926.1' => 'oeu', 'Oeu043121.2' => 'oeu', 'Oeu043597.1' => 'oeu', 'Oeu049134.1' => 'oeu', 'Oeu053500.1' => 'oeu', 'Os01g0730900' => 'osa', 'Os05g0529600' => 'osa', 'Os08g0120200' => 'osa', 'Os11g0244300' => 'osa', 'Os12g0209300' => 'osa', 'Os12g0289600' => 'osa', 'Peaxi162Scf00089g00938' => 'pax', 'Peaxi162Scf00112g00048' => 'pax', 'Peaxi162Scf00194g01049' => 'pax', 'PGR031G3259' => 'pgr', 'PGR044G1551' => 'pgr', 'PGR083G0685' => 'pgr', 'PGR142G3909' => 'pgr', 'PGSC0003DMG400015161' => 'stu', 'PGSC0003DMG400018259' => 'stu', 'PGSC0003DMG400028463' => 'stu', 'Phvul.003G090800' => 'pvu', 'Phvul.003G207500' => 'pvu', 'Phvul.006G172900' => 'pvu', 'Phvul.009G170400' => 'pvu', 'Potri.003G044900' => 'ptr', 'Potri.004G061700' => 'ptr', 'Potri.004G230300' => 'ptr', 'Potri.011G071300' => 'ptr', 'Potri.012G091700' => 'ptr', 'Potri.015G088100' => 'ptr', 'Pp3c13_13940' => 'ppa', 'Pp3c1_35800' => 'ppa', 'Pp3c26_6700' => 'ppa', 'Pp3c3_17400' => 'ppa', 'Pp3c3_17520' => 'ppa', 'Pp3c4_17210' => 'ppa', 'Pp3c9_18380' => 'ppa', 'Prupe.1G586700' => 'ppe', 'Prupe.4G067700' => 'ppe', 'Prupe.5G160500' => 'ppe', 'Psat0s2555g0240' => 'psa', 'Psat1g194560' => 'psa', 'Psat4g063880' => 'psa', 'Psat5g141040' => 'psa', 'PSO017G3776' => 'pso', 'PSO017G4404' => 'pso', 'PSO063G0927' => 'pso', 'PSO170G2433' => 'pso', 'PSO170G5389' => 'pso', 'PSO170G6121' => 'pso', 'PSO210G3331' => 'pso', 'PSO447G0240' => 'pso', 'PSO782G1855' => 'pso', 'QL02p056630' => 'qlo', 'QL02p103695' => 'qlo', 'QL05p050035' => 'qlo', 'QL10p005693' => 'qlo', 'RcHm_v2.0_Chr2g0146641' => 'rch', 'RcHm_v2.0_Chr5g0011921' => 'rch', 'RcHm_v2.0_Chr7g0191751' => 'rch', 'RcHm_v2.0_Chr7g0217971' => 'rch', 'RcHm_v2.0_Chr7g0218871' => 'rch', 'RcHm_v2.0_Chr7g0232131' => 'rch', 'Rhsim11G0115200' => 'rsi', 'Rhsim13G0187200' => 'rsi', 'Sabra01G0175600' => 'sbr', 'Sabra03G0021800' => 'sbr', 'Sabra11G0055900' => 'sbr', 'Sabra11G0059000' => 'sbr', 'Sabra12G0066400' => 'sbr', 'SalBow7G4630' => 'sbo', 'SalBow7G4755' => 'sbo', 'SalBow8G2953' => 'sbo', 'SalBow8G2987' => 'sbo', 'Sc04g0001140' => 'sci', 'Sc05g0006830' => 'sci', 'Sc07g0003280' => 'sci', 'Sed0001864' => 'sed', 'Sed0006113' => 'sed', 'Sed0022831' => 'sed', 'Sed0022889' => 'sed', 'SEGI_06658' => 'sgi', 'SEGI_14100' => 'sgi', 'SEGI_21418' => 'sgi', 'SEGI_27293' => 'sgi', 'SEGI_28438' => 'sgi', 'SEGI_31843' => 'sgi', 'SEGI_32843' => 'sgi', 'SEGI_37291' => 'sgi', 'SEGI_40104' => 'sgi', 'SEGI_41078' => 'sgi', 'SGA_v2.0_scaffold100G29556' => 'sas', 'SGA_v2.0_scaffold106G30604' => 'sas', 'SGA_v2.0_scaffold123G33477' => 'sas', 'SGA_v2.0_scaffold254G45230' => 'sas', 'SGA_v2.0_scaffold25G10786' => 'sas', 'SGA_v2.0_scaffold81G26053' => 'sas', 'SHI50870' => 'shi', 'SMO198G0102' => 'smo', 'SMO356G0565' => 'smo', 'Solyc01g102810.3' => 'sly', 'Solyc02g072090.2' => 'sly', 'Solyc03g111680.3' => 'sly', 'Sopen01g045210' => 'spe', 'Sopen02g021050' => 'spe', 'Sopen03g030800' => 'spe', 'Sp1g12830' => 'spa', 'Sp2g10610' => 'spa', 'Sp2g13710' => 'spa', 'Sp7g17530' => 'spa', 'Sp7g22770' => 'spa', 'TAR381G0431' => 'tar', 'TAR624G1016' => 'tar', 'TAR626G1395' => 'tar', 'TAR629G0985' => 'tar', 'THA.LOC104798436' => 'tha', 'THA.LOC104805130' => 'tha', 'THA.LOC104811607' => 'tha', 'THA.LOC104825000' => 'tha', 'Thecc.03G120000' => 'tca', 'Thecc.06G063600' => 'tca', 'Thecc.06G164600' => 'tca', 'Thhalv10000763m.g' => 'esa', 'Thhalv10003531m.g' => 'esa', 'Thhalv10006609m.g' => 'esa', 'Thhalv10024266m.g' => 'esa', 'Thhalv10024379m.g' => 'esa', 'TPR.G37499' => 'tpr', 'TPR.G37577' => 'tpr', 'TPR.G38650' => 'tpr', 'TPR.G4468' => 'tpr', 'TPR.G5938' => 'tpr', 'TWI09G0472' => 'twi', 'TWI14G1109' => 'twi', 'TWI23G0013' => 'twi', 'TWI39G0685' => 'twi', 'TWI53G0488' => 'twi', 'TWI59G1151' => 'twi', 'unitig_26.g9612' => 'ugi', 'unitig_61.g26466' => 'ugi', 'unitig_699.g19837' => 'ugi', 'unitig_699.g19838' => 'ugi', 'unitig_747.g21280' => 'ugi', 'unitig_749.g13667' => 'ugi', 'unitig_749.g13668' => 'ugi', 'vmacro01625' => 'vma', 'vmacro04000' => 'vma', 'vmacro16695' => 'vma', 'VMungo0540G0601' => 'vmu', 'VMungo1215G0189' => 'vmu', 'VMungo1215G2764' => 'vmu', 'VMungo1309G0687' => 'vmu', 'Zm00001eb004960' => 'zma', 'Zm00001eb057220' => 'zma', 'Zm00001eb079340' => 'zma', 'Zm00001eb151550' => 'zma', 'Zm00001eb154140' => 'zma', 'Zm00001eb157320' => 'zma', 'Zm00001eb173480' => 'zma', 'Zm00001eb293320' => 'zma', 'Zm00001eb361980' => 'zma', 'Zm00001eb411140' => 'zma', 'Zm00001eb425120' => 'zma' ) $gf_id = 'HOM05D001195' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001195' ) $data_identifier = 'HOM05D001195' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 9, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 9, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 12, 'mes' => (int) 8, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 6, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 10, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 11 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb425120' $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